MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 5458 to 5507 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2729	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	Divided	5333	5351.61	1.00349
2730	myelin gene expression factor 2. [refseq;acc:nm_016132]		5214.9	5197.18	1.00341
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Subtracted	4113.79	4095.53	18.26
2731	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]
	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	Divided	7913.63	7939.94	1.00332
2732	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	Subtracted	4113.79	4095.53	18.26
	transcription factor relb (i-rel). [swissprot;acc:q01201]	Divided	7913.63	7939.94	1.00332
2733	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	Subtracted	4113.79	4095.53	18.26
	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	Divided	7913.63	7939.94	1.00332
2734	60s ribosomal protein l18. [swissprot;acc:q07020]	Subtracted	4113.79	4095.53	18.26
	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]	Divided	7913.63	7939.94	1.00332
2735	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]		8991.87	9019.99	1.00313
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Subtracted	5214.9	5197.18	17.72
2736	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	Divided	4887.59	4902.08	1.00296
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Subtracted	4163.36	4145.95	17.41
2737	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]		4137.61	4152.72	15.11
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Divided	4486.83	4499.52	1.00283
2738	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	Subtracted	4887.59	4902.08	14.49
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Divided	4486.83	4499.52	1.00283
2739	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]		4877.74	4890.64	1.00264
		Subtracted			12.9
2740	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	Divided	4200.59	4210.94	1.00246
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Subtracted	4486.83	4499.52	12.69
2741	sorting nexin 5. [swissprot;acc:q9y5x3]	Divided	5339.67	5327.2	1.00234
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Subtracted	4486.83	4499.52	12.69
2742	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Divided	10198.1	10174.3	1.00234
	sorting nexin 5. [swissprot;acc:q9y5x3]	Subtracted	5339.67	5327.2	12.47
2743	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	Divided	4824.49	4813.92	1.0022
	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	Subtracted	7746.61	7757.23	10.62
2744	60s acidic ribosomal protein p2. [swissprot;acc:p05387]		4824.49	4813.92	10.57
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Divided	10143.6	10163.6	1.00197
2745	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	Subtracted	4200.59	4210.94	10.35
	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	Divided	7746.61	7757.23	1.00137
2746	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	Subtracted	7776.91	7783.48	6.57
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Divided	4188.5	4194.22	1.00137
2747	putatative 28 kda protein. [refseq;acc:nm_020143]		4708.68	4702.58	1.0013
		Subtracted			6.1
2748	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]		4188.5	4194.22	5.72
	syntaxin 6. [swissprot;acc:o43752]	Divided	5296.39	5301.11	1.00089
2749	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]		7776.91	7783.48	1.00084
	syntaxin 6. [swissprot;acc:o43752]	Subtracted	5296.39	5301.11	4.72
2750	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	5294.28	5298.42	1.00078
		Subtracted			4.14
2751	tripartite motif protein 2. [swissprot;acc:q9c040]	Divided	7810.47	7812.55	1.00027
		Subtracted			2.08
2752	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Divided	4521.42	4521.87	1.0001
		Subtracted			0.45
2753	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Divided			1.0001
		Subtracted			0.45
2754	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Divided			1.0001

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.